The first step in physical genome mapping and analysis is to demonstrate ultra high molecular weight DNA extraction and analysis procedures. This has previously been demonstrated for only two types of insects, mosquitoes and members of the genus Drosophila. I have modified previously published procedures to achieve reproducible isolation of megabase-sized DNA from queen honey bee ovaries. Furthermore, this DNA is stable during storage at 4°C for more than one year, is readily digested with restriction enzymes and is not prone to degradation by contaminating nucleases. The ovaries from a single queen produced enough DNA for 20 to 30 digestion reactions.